Moray, I'm trying to understand this. If the tree is monoecious, then it has male and female flowers. Why isn't it self-fertile?...
I was also wondering, though, about the innoculation of the blight fungal pathogen to determine resistance. You said that this breeding orchard innoculated trees in an effort to determine resistance. How is this controlled?
Good questions. I suppose there are two answers to the self-fertile question, one mechanical and the other evolutionary. The evolutionary answer is pretty straightforward: one of the major purported benefits of sexual reproduction--genetic diversity of offspring--is somewhat diminished if a plant pollinates itself. One could speculate that dioecious plants came about because plants with only one flower type absolutely could not pollinate themselves. It is worth noting that, by analogy, animals are almost without exception "dioecious".
I wish I had a list of examples right at hand to illustrate the point, but I believe it is actually quite common that a plant goes to some pains to avoid self pollination. Even in plants with perfect flowers there are often barriers to self pollination. Orchids, for example, represent a huge group whose flowers have a shape that makes self pollination very difficult. The mechanical and chemical means to prevent self pollination could include timing pollen release before the stigmas are ready to receive pollen, chemical markers on the pollen that the stigmas recognize as "self", and so on. Suffice it to say, in the case of American chestnut self pollination is very rare.
To challenge hybrid orchard plants with the blight, a small hole is drilled a half inch or so into the trunk of each tree a couple of feet above the ground. Fungal innoculum is smeared into the hole, and the hole is plugged. A few months later (there is an exact protocol for all this, but I don't know the details) all the challenged trees are inspected and rated from 1 to 5 according to severity of the resulting blight canker. Only the trees with the smallest cankers are kept for breeding the next year. Apparently they will survive long enough to produce pollen, or maybe even nuts, and so the chain remains unbroken. As far as I am aware, the blight is lethal to all hybrids because, at best, they can have only half the Chinese resistance genes.
The pictures below show part of an orchard of 9-yr-old trees, a closer view of a tree showing its size (about 5 inches in diameter), and a closeup showing a sunken blight canker a couple of days after inspection. The arrow points to the site of innoculation. I believe that it was a relatively large canker, indicating the tree had very little resistance and was a candidate to be culled.